## ----message=FALSE, warning=FALSE---------------------------------------------------------------------------
library(OmnipathR)

## ----chalmers-raw-------------------------------------------------------------------------------------------
ch_raw <- chalmers_gem_raw()

## ----chalmers-proc------------------------------------------------------------------------------------------
ch_processed <- chalmers_gem()
names(ch_processed)

## ----chalmers-id--------------------------------------------------------------------------------------------
ch_met <- chalmers_gem_metabolites()

ch_met

## ----chalmers-idtrans, eval = FALSE-------------------------------------------------------------------------
#  translate_ids('MAM00001', 'metabolicatlas', 'recon3d', chalmers = TRUE)

## ----chalmers, eval = FALSE---------------------------------------------------------------------------------
#  ch <- chalmers_gem_network()
#  
#  ch

## ----stitch-actions, eval = FALSE---------------------------------------------------------------------------
#  sta <- stitch_actions()
#  
#  sta

## ----stitch-links, eval = FALSE-----------------------------------------------------------------------------
#  stl <- stitch_links()
#  
#  stl

## ----stitch, eval = FALSE-----------------------------------------------------------------------------------
#  st <- stitch_network()
#  
#  st

## ----omnipath-----------------------------------------------------------------------------------------------
op <- omnipath_for_cosmos()

op

## ----cosmos, eval = FALSE-----------------------------------------------------------------------------------
#  pkn <- cosmos_pkn()
#  
#  pkn

## ----session------------------------------------------------------------------------------------------------
sessionInfo()